Graphviz— Open Source Graph Drawing Tools

Ellson, J.; Gansner, Emden R.; Koutsofios, Lefteris; North, Stephen C.; Woodhull, Gordon

doi:10.1007/3-540-45848-4_57

Cited by 510 publications

(376 citation statements)

References 1 publication

Supporting

Mentioning

354

Contrasting

Unclassified

Order By: Relevance

“…The client process displays the tree structures and supports functions, such as searching by ID and changing leaf attributes: circle size, colored border and biochemical metric mapped to the circle. Layout optimization uses a multi-scale version of dynamic, spring-model layouts implemented in GraphViz (Ellson et al, 2001). This allows users to actively pull and reorient nodes/branches to improve the visual layout in a local area.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets

Lü¹,

Carlson

2016

Bioinformatics

View full text Add to dashboard Cite

Motivation: What if you could explain complex chemistry in a simple tree and share that data online with your collaborators? Computational biology often incorporates diverse chemical data to probe a biological question, but the existing tools for chemical data are ill-suited for the very large datasets inherent to bioinformatics. Furthermore, existing visualization methods often require an expert chemist to interpret the patterns. Biologists need an interactive tool for visualizing chemical information in an intuitive, accessible way that facilitates its integration into today's team-based biological research. Results: ChemTreeMap is an interactive, bioinformatics tool designed to explore chemical space and mine the relationships between chemical structure, molecular properties, and biological activity. ChemTreeMap synergistically combines extended connectivity fingerprints and a neighbor-joining algorithm to produce a hierarchical tree with branch lengths proportional to molecular similarity. Compound properties are shown by leaf color, size and outline to yield a user-defined visualization of the tree. Two representative analyses are included to demonstrate ChemTreeMap's capabilities and utility: assessing dataset overlap and mining structure-activity relationships. Availability and Implementation: The examples from this paper may be accessed at http://ajing. github.io/ChemTreeMap/. Code for the server and client are available in the Supplementary Information, at the aforementioned github site, and on Docker Hub (https://hub.docker.com) with the nametag ajing/chemtreemap.

show abstract

Section: Methodsmentioning

confidence: 99%

“…GraphViz and RapidNJ are freely available online for major operating systems (Ellson et al, 2001;Simonsen et al, 2008). The graphics can be viewed on any computer with an HTML5 capable browser (tested on Google Chrome Version 46, Internet Explorer 11, and Safari 9.0).…”

Section: Methodsmentioning

confidence: 99%

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets

Lü¹,

Carlson

2016

Bioinformatics

View full text Add to dashboard Cite

show abstract

“…It makes sense to use representations familiar to software engineers similar to entity-relationship diagrams. There is a wealth of tool support for graphical modelling [38,19] that can be adapted for this purpose.…”

Section: Future Workmentioning

confidence: 99%

A descriptive type foundation for RDF Schema

Ciobanu

Horne

Sassone

2016

Journal of Logical and Algebraic Methods in Programming

View full text Add to dashboard Cite

This paper provides a type theoretic foundation for descriptive types that appear in Linked Data. Linked Data is data published on the Web according to principles and standards supported by the W3C. Such Linked Data is inherently messy: this is due to the fact that instead of being assigned a strict a priori schema, the schema is inferred a posteriori. Moreover, such a posteriori schema consists of opaque names that guide programmers, without prescribing structure. We employ what we call a descriptive type system for Linked Data. This descriptive type system differs from a traditional type system in that it provides hints or warnings rather than errors and evolves to describe the data while Linked Data is discovered at runtime. We explain how our descriptive type system allows RDF Schema inference mechanisms to be tightly coupled with domain specific scripting languages for Linked Data, enabling an interactive feedback to Web developers.

show abstract

“…5. We developed a plugin to produce graphical visualizations of IOPT states after simulation and verification by using the GraphViz solution [9]. This represents the case where the system just allows the firing of one actuator that disables according to the priorities one enabled module from many (defined as n=1 in the place waitingToEnable) when sensors were fired concurrently.…”

Section: Simulation and Verificationmentioning

confidence: 99%

SysVeritas: A Framework for Verifying IOPT Nets and Execution Semantics within Embedded Systems Design

Barbosa

Barros

Ramalho

et al. 2011

Technological Innovation for Sustainability

View full text Add to dashboard Cite

Abstract. We present a rewriting logic based technique for defining the formal executable semantics of a non-autonomous Petri net class, named Input-Output Place/Transition nets (IOPT nets), designed for model-based embedded system's development, according to the MDA initiative. For this purpose, we provide model-to-model transformations from ecore IOPT models to a rewriting logic specification in Maude. The transformations are defined as semantic mappings based on the respective metamodels: the IOPT metamodel and the Maude metamodel. Also, we define model to-text transformations for the generation of the model execution code in the rewriting logic framework. Hence, we present a translational semantics composed by two components: (i) the denotational one, considering as semantic domains the operations, equations, and properties that specify the Petri net structure, signals, and events according to the commutative monoid view; and (ii) the operational one, that changes the interleaving semantics of Maude using rewriting rules specified at the Maude metalevel to provide a maximal step semantics for transitions with arcs, test arcs, and priorities. Additionally, this work gives architectural advices in order to compose new semantics specifications by simple component substitution. Due to its simulation and verification capabilities for control systems, the presented work was applied to a domotic project that intends to save energy in residential buildings.

show abstract

Graphviz— Open Source Graph Drawing Tools

Cited by 510 publications

References 1 publication

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets

A descriptive type foundation for RDF Schema

SysVeritas: A Framework for Verifying IOPT Nets and Execution Semantics within Embedded Systems Design

Contact Info

Product

Resources

About